Difference between revisions of "Documentation/Nightly/Extensions/SkeletalRepresentation"
From Slicer Wiki
(update terms) |
|||
| (7 intermediate revisions by the same user not shown) | |||
| Line 2: | Line 2: | ||
'''Acknowledgements:''' This work is part of Slicer Shape Analysis Toolbox ([http://salt.slicer.org/ SlicerSALT]), funded by NIH NIBIB R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects), as well as the [https://www.slicer.org/ Slicer community].<br /> | '''Acknowledgements:''' This work is part of Slicer Shape Analysis Toolbox ([http://salt.slicer.org/ SlicerSALT]), funded by NIH NIBIB R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects), as well as the [https://www.slicer.org/ Slicer community].<br /> | ||
| − | '''Author:''' Zhiyuan Liu<br /> | + | '''Author:''' [http://www.cs.unc.edu/~zhiy/ Zhiyuan Liu]<br /> |
| − | '''Contributors:''' Pablo Hernandez-Cerdan, Jean-Christophe Fillion-Robin, Beatriz Paniagua, Jared Vicory, Junpyo Hong, Stephen M. Pizer<br /> | + | '''Contributors:''' Pablo Hernandez-Cerdan, [https://www.kitware.com/jean-christophe-fillion-robin/ Jean-Christophe Fillion-Robin], [https://www.kitware.com/beatriz-paniagua/ Beatriz Paniagua], [https://www.kitware.com/jared-vicory/ Jared Vicory], Junpyo Hong, [http://www.cs.unc.edu/~smp/ Stephen M. Pizer]<br /> |
'''Contact:''' Zhiyuan Liu, zhiy at cs dot unc dot edu | '''Contact:''' Zhiyuan Liu, zhiy at cs dot unc dot edu | ||
== Extension Description == | == Extension Description == | ||
| − | This extension is an open source tool to | + | This extension is an open source tool to initialize, refine and visualize [http://midag.cs.unc.edu/pubs/papers/xavier_book_2019.pdf skeletal representation] (abbreviated as s-rep) of 3D objects in biomedical images. The main features of this extension include:<br /> |
| − | * | + | * Initialize an s-rep by mean curvature flow of an object boundary<br /> |
| − | * Refine an s-rep to fit an object boundary | + | * Refine an s-rep to fit an object boundary<br /> |
| + | * Visualize the s-rep | ||
| + | S-reps have a number of advantages in shape analysis of human organs. Some previous research has shown the superiority of using s-reps to perform hypothesis testing, classification and shape distribution analysis. | ||
<gallery> | <gallery> | ||
SkeletalRepresentation.png|Icon of the extension | SkeletalRepresentation.png|Icon of the extension | ||
| Line 16: | Line 18: | ||
== Modules == | == Modules == | ||
* Skeletal Representation Initializer | * Skeletal Representation Initializer | ||
| − | * Skeletal Representation | + | * Skeletal Representation Refiner |
* Skeletal Representation Visualizer | * Skeletal Representation Visualizer | ||
| + | |||
== Use Cases == | == Use Cases == | ||
Sample data can be found [https://github.com/KitwareMedical/SlicerSkeletalRepresentation/blob/master/SkeletalRepresentationVisualizer/Testing/test_data/hippo.m3d here].<br /> | Sample data can be found [https://github.com/KitwareMedical/SlicerSkeletalRepresentation/blob/master/SkeletalRepresentationVisualizer/Testing/test_data/hippo.m3d here].<br /> | ||
| Line 23: | Line 26: | ||
Hippo_mesh.png|The surface mesh of hippocampus | Hippo_mesh.png|The surface mesh of hippocampus | ||
New_srep.png|Visualize the s-rep of the hippocampus | New_srep.png|Visualize the s-rep of the hippocampus | ||
| + | Initialize.png|Initialize the s-rep of the hippocampus | ||
</gallery> | </gallery> | ||
== Tutorials == | == Tutorials == | ||
<gallery> | <gallery> | ||
| − | Srep_tutorial.png| | + | Srep_tutorial.png|Tutorial for visualization |
| + | Srep_tutorial.png|Tutorial for initialization | ||
| + | Srep_tutorial.png|Tutorial for refinement | ||
</gallery> | </gallery> | ||
| Line 34: | Line 40: | ||
== References == | == References == | ||
* Stephen M. Pizer, Junpyo Hong, Jared Vicory, J. S. Marron, and others, "[http://midag.cs.unc.edu/pubs/papers/xavier_book_2019.pdf Object Shape Representation via Skeletal Models (s-reps) and Statistical Analysis]" in Riemannian Geometric Statistics in Medical Image Analysis, no. (Xavier Pennec, Stefan Sommer, and Tom Fletcher, eds.), 2019. | * Stephen M. Pizer, Junpyo Hong, Jared Vicory, J. S. Marron, and others, "[http://midag.cs.unc.edu/pubs/papers/xavier_book_2019.pdf Object Shape Representation via Skeletal Models (s-reps) and Statistical Analysis]" in Riemannian Geometric Statistics in Medical Image Analysis, no. (Xavier Pennec, Stefan Sommer, and Tom Fletcher, eds.), 2019. | ||
| + | * Source code can be found https://github.com/KitwareMedical/SlicerSkeletalRepresentation | ||
Latest revision as of 01:16, 23 October 2019
Home < Documentation < Nightly < Extensions < SkeletalRepresentationContents
Introduction and Acknowledgements
Acknowledgements: This work is part of Slicer Shape Analysis Toolbox (SlicerSALT), funded by NIH NIBIB R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects), as well as the Slicer community.
Author: Zhiyuan Liu
Contributors: Pablo Hernandez-Cerdan, Jean-Christophe Fillion-Robin, Beatriz Paniagua, Jared Vicory, Junpyo Hong, Stephen M. Pizer
Contact: Zhiyuan Liu, zhiy at cs dot unc dot edu
Extension Description
This extension is an open source tool to initialize, refine and visualize skeletal representation (abbreviated as s-rep) of 3D objects in biomedical images. The main features of this extension include:
- Initialize an s-rep by mean curvature flow of an object boundary
- Refine an s-rep to fit an object boundary
- Visualize the s-rep
S-reps have a number of advantages in shape analysis of human organs. Some previous research has shown the superiority of using s-reps to perform hypothesis testing, classification and shape distribution analysis.
Icon of the extension
Modules
- Skeletal Representation Initializer
- Skeletal Representation Refiner
- Skeletal Representation Visualizer
Use Cases
Sample data can be found here.
The surface mesh of hippocampus
Visualize the s-rep of the hippocampus
Initialize the s-rep of the hippocampus
Tutorials
Tutorial for visualization
Tutorial for initialization
Tutorial for refinement
Similar Extensions
NA
References
- Stephen M. Pizer, Junpyo Hong, Jared Vicory, J. S. Marron, and others, "Object Shape Representation via Skeletal Models (s-reps) and Statistical Analysis" in Riemannian Geometric Statistics in Medical Image Analysis, no. (Xavier Pennec, Stefan Sommer, and Tom Fletcher, eds.), 2019.
- Source code can be found https://github.com/KitwareMedical/SlicerSkeletalRepresentation
